rs17816376

chr15-89690322-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003847.3(PEX11A):c.56+255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,186 control chromosomes in the GnomAD database, including 2,604 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2604 hom., cov: 32)
• Consequence: PEX11A NM_003847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

PEX11A (HGNC:8852): (peroxisomal biogenesis factor 11 alpha) This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

WDR93 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEX11A	NM_003847.3	c.56+255A>G		intron_variant		ENST00000300056.8
PEX11A	NM_001271572.2	c.56+255A>G		intron_variant
PEX11A	NM_001271573.2	c.-264+255A>G		intron_variant
WDR93	XM_011521794.3			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX11A	ENST00000300056.8	c.56+255A>G		intron_variant		1	NM_003847.3	P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27132 AN: 152068 Hom.: 2605 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.178 AC: 27131 AN: 152186 Hom.: 2604 Cov.: 32 AF XY: 0.176 AC XY: 13073 AN XY: 74394

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.191

Alfa AF: 0.203 Hom.: 6450

Bravo AF: 0.174

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.7
Dann	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17816376; hg19: chr15-90233553;